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AIMP1

aminoacyl tRNA synthetase complex interacting multifunctional protein 1, the group of Aminoacyl tRNA synthetase complex interacting multifunctional proteins

Basic information

Region (hg38): 4:106315543-106349456

Previous symbols: [ "SCYE1" ]

Links

ENSG00000164022NCBI:9255OMIM:603605HGNC:10648Uniprot:Q12904AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • hypomyelinating leukodystrophy 3 (Strong), mode of inheritance: AR
  • hypomyelinating leukodystrophy 3 (Moderate), mode of inheritance: AR
  • autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
  • hypomyelinating leukodystrophy 3 (Supportive), mode of inheritance: AR
  • hypomyelinating leukodystrophy 3 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Leukodystrophy, hypomyelinating, 3ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic21092922; 21397066; 21397067; 24958424

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AIMP1 gene.

  • not provided (71 variants)
  • Inborn genetic diseases (16 variants)
  • Hypomyelinating leukodystrophy 3 (10 variants)
  • AIMP1-related condition (2 variants)
  • Hypotonia (1 variants)
  • not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AIMP1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
9
clinvar
2
clinvar
11
missense
36
clinvar
2
clinvar
2
clinvar
40
nonsense
2
clinvar
1
clinvar
3
start loss
1
clinvar
1
clinvar
2
frameshift
6
clinvar
1
clinvar
1
clinvar
8
inframe indel
3
clinvar
3
splice donor/acceptor (+/-2bp)
1
clinvar
1
clinvar
2
splice region
1
1
2
non coding
1
clinvar
4
clinvar
3
clinvar
9
clinvar
17
Total 9 3 46 15 13

Highest pathogenic variant AF is 0.0000657

Variants in AIMP1

This is a list of pathogenic ClinVar variants found in the AIMP1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
4-106316238-C-T Benign (Nov 10, 2018)1272300
4-106316331-C-T Benign (Jun 19, 2021)1243501
4-106316548-A-G not specified Uncertain significance (Mar 13, 2023)2501160
4-106316550-G-C Uncertain significance (Feb 01, 2018)809652
4-106316586-C-T AIMP1-related condition Likely benign (Aug 09, 2019)3034702
4-106316858-A-G Benign (Jun 18, 2021)1283130
4-106324979-C-A Benign (Nov 10, 2018)1279491
4-106325015-AAAT-A Hypomyelinating leukodystrophy 3 Uncertain significance (Dec 02, 2021)1497296
4-106325019-A-G Inborn genetic diseases Uncertain significance (Feb 16, 2023)2479892
4-106325033-G-C Benign (Jan 29, 2024)1169308
4-106325076-G-C Uncertain significance (Aug 31, 2022)2008274
4-106325078-A-C Uncertain significance (Mar 01, 2022)2169401
4-106325080-A-T Inborn genetic diseases Uncertain significance (Aug 01, 2022)1431757
4-106325086-AG-A Pathogenic (Aug 10, 2022)2088801
4-106325091-C-T Hypotonia Pathogenic (-)1172642
4-106325096-TTCTC-T Pathogenic (Jul 21, 2022)2017299
4-106325105-T-C Likely benign (Sep 27, 2022)1978153
4-106327456-C-T Hypomyelinating leukodystrophy 3 • AIMP1-related condition Pathogenic/Likely pathogenic (Jan 26, 2023)162377
4-106327466-T-C Uncertain significance (Jul 27, 2022)1950184
4-106327486-C-T Pathogenic (Feb 24, 2023)2576924
4-106327487-G-A Uncertain significance (Jul 14, 2022)1901311
4-106327500-TA-T Hypomyelinating leukodystrophy 3 Pathogenic (Oct 25, 2023)590774
4-106327531-CAA-C Hypomyelinating leukodystrophy 3 Pathogenic (Nov 02, 2023)2159413
4-106327553-T-A Uncertain significance (Jun 28, 2022)1436698
4-106327564-G-A Uncertain significance (Jul 11, 2022)1304676

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
AIMP1protein_codingprotein_codingENST00000394701 733683
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
3.04e-70.5411257080371257450.000147
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.2071821741.040.000008552198
Missense in Polyphen4561.7790.7284852
Synonymous0.5005559.90.9180.00000311645
Loss of Function0.9231216.00.7518.07e-7200

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001160.000116
Ashkenazi Jewish0.0001990.000198
East Asian0.0001090.000109
Finnish0.00009240.0000924
European (Non-Finnish)0.0001590.000158
Middle Eastern0.0001090.000109
South Asian0.0002290.000229
Other0.0003270.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Non-catalytic component of the multisynthase complex. Stimulates the catalytic activity of cytoplasmic arginyl-tRNA synthase (PubMed:10358004). Binds tRNA. Possesses inflammatory cytokine activity (PubMed:11306575). Negatively regulates TGF-beta signaling through stabilization of SMURF2 by binding to SMURF2 and inhibiting its SMAD7-mediated degradation (By similarity). Involved in glucose homeostasis through induction of glucagon secretion at low glucose levels (By similarity). Promotes dermal fibroblast proliferation and wound repair (PubMed:16472771). Regulates KDELR1-mediated retention of HSP90B1/gp96 in the endoplasmic reticulum (By similarity). Plays a role in angiogenesis by inducing endothelial cell migration at low concentrations and endothelian cell apoptosis at high concentrations (PubMed:12237313). Induces maturation of dendritic cells and monocyte cell adhesion (PubMed:11818442). Modulates endothelial cell responses by degrading HIF-1A through interaction with PSMA7 (PubMed:19362550). {ECO:0000250|UniProtKB:P31230, ECO:0000269|PubMed:10358004, ECO:0000269|PubMed:11157763, ECO:0000269|PubMed:11306575, ECO:0000269|PubMed:11818442, ECO:0000269|PubMed:12237313, ECO:0000269|PubMed:19362550}.;
Disease
DISEASE: Leukodystrophy, hypomyelinating, 3 (HLD3) [MIM:260600]: A severe autosomal recessive hypomyelinating leukodystrophy characterized by early infantile onset of global developmental delay, lack of development, lack of speech acquisition, and peripheral spasticity associated with decreased myelination in the central nervous system. {ECO:0000269|PubMed:21092922}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
tRNA Aminoacylation;Translation;Metabolism of proteins;Metabolism of amino acids and derivatives;Metabolism;Selenoamino acid metabolism;SeMet incorporation into proteins;Cytosolic tRNA aminoacylation (Consensus)

Recessive Scores

pRec
0.159

Intolerance Scores

loftool
0.976
rvis_EVS
0.08
rvis_percentile_EVS
60.31

Haploinsufficiency Scores

pHI
0.0933
hipred
Y
hipred_score
0.579
ghis
0.607

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.477

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Aimp1
Phenotype
homeostasis/metabolism phenotype; immune system phenotype;

Gene ontology

Biological process
angiogenesis;negative regulation of endothelial cell proliferation;tRNA aminoacylation for protein translation;apoptotic process;chemotaxis;inflammatory response;cell adhesion;signal transduction;cell-cell signaling;response to wounding;regulation of signaling receptor activity;leukocyte migration;defense response to virus;positive regulation of glucagon secretion
Cellular component
extracellular space;nucleus;endoplasmic reticulum;Golgi apparatus;cytosol;cell surface;membrane;aminoacyl-tRNA synthetase multienzyme complex;methionyl glutamyl tRNA synthetase complex
Molecular function
tRNA binding;cytokine activity;protein binding;protein homodimerization activity;GTPase binding